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import unittest
from ost import io, mol
class TestNonStandard(unittest.TestCase):
def test_fastModified(self):
# phoshoserine: test if we correctly strip off modifications
tpl=io.LoadPDB('testfiles/sep.pdb')
new_hdl=mol.CreateEntity();
ed=new_hdl.EditXCS()
c=ed.InsertChain('A')
ed.AppendResidue(c, 'SER')
err, has_cbeta=mol.alg.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed)
self.assertTrue(err)
self.assertTrue(has_cbeta)
residues=new_hdl.residues
self.assertEqual(len(residues), 1)
self.assertEqual(len(residues[0].atoms), 6)
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "N").IsValid())
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CA").IsValid())
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "C").IsValid())
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "O").IsValid())
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CB").IsValid())
self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "OG").IsValid())
def test_CBeta(self):
# test if the dst residues contain cbeta, unless they are glycines
tpl=io.LoadPDB('testfiles/cbeta.pdb')
new_hdl=mol.CreateEntity();
ed=new_hdl.EditXCS()
c=ed.InsertChain('A')
ed.AppendResidue(c, 'MET')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'HIS')
err, has_cbeta=mol.alg.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed)
self.assertTrue(has_cbeta)
self.assertTrue(err)
err, has_cbeta=mol.alg.CopyConserved(tpl.residues[1], new_hdl.residues[1], ed)
self.assertFalse(has_cbeta)
self.assertTrue(err)
err, has_cbeta=mol.alg.CopyConserved(tpl.residues[2], new_hdl.residues[2], ed)
self.assertFalse(has_cbeta)
self.assertTrue(err)
err, has_cbeta=mol.alg.CopyConserved(tpl.residues[3], new_hdl.residues[3], ed)
self.assertTrue(has_cbeta)
self.assertTrue(err)
residues=new_hdl.residues
self.assertEqual(len(residues), 4)
self.assertTrue(residues[0].FindAtom("CB").IsValid())
self.assertFalse(residues[1].FindAtom("CB").IsValid())
self.assertFalse(residues[2].FindAtom("CB").IsValid())
self.assertTrue(residues[3].FindAtom("CB").IsValid())
def test_CBetaFail(self):
# make sure that we can handle cases where CB reconstruction fails
# NOTES:
# - SNN is (since June 2011) labeled as a modified ASN but has a weird
# backbone structure without any overlap in atom names with ASN
# -> we hence expect it to a) always fall back to CopyNonConserved
# and b) fail to copy any atoms (and hence also fail to)
# - SNN also removes N of following residue which is expected to have an
# incomplete backbone which would make it impossible to create a CB pos.
# source of file: residues A.198 and A.199 from PDB ID 2YHW
tpl = io.LoadPDB('testfiles/cbeta_fail.pdb')
new_hdl = mol.CreateEntity();
ed = new_hdl.EditXCS()
c = ed.InsertChain('A')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'ALA')
ed.AppendResidue(c, 'ASN')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'ALA')
# SNN to GLY
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
self.assertFalse(err)
self.assertEqual(new_hdl.residues[0].atom_count, 0)
# SNN to ALA
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[1], ed)
self.assertFalse(err)
self.assertEqual(new_hdl.residues[1].atom_count, 0)
# SNN to ASN
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[2], ed)
self.assertFalse(err)
self.assertEqual(new_hdl.residues[2].atom_count, 0)
# GLY to GLY
err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[3], ed)
self.assertTrue(err)
self.assertEqual(new_hdl.residues[3].atom_count, 3)
self.assertFalse(new_hdl.residues[3].FindAtom("CB").IsValid())
# GLY to ALA
err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[4], ed)
self.assertFalse(err)
self.assertEqual(new_hdl.residues[4].atom_count, 3)
self.assertFalse(new_hdl.residues[4].FindAtom("CB").IsValid())
def test_CopyResidue(self):
tpl = io.LoadPDB('testfiles/cbeta.pdb')
new_hdl = mol.CreateEntity();
ed = new_hdl.EditXCS()
c = ed.InsertChain('A')
ed.AppendResidue(c, 'MET')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'HIS')
ed.AppendResidue(c, 'HIS')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'HIS')
ed.AppendResidue(c, 'MET')
# MET to MET
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
self.assertTrue(err)
#GLY to GLY
err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
self.assertTrue(err)
# GLY to GLY
err = mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
self.assertTrue(err)
#now we copy a HIS to a HIS
err = mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
self.assertTrue(err)
# copy a GLY to a HIS
err, has_cbeta = mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
self.assertFalse(has_cbeta)
# copy a MET to a GLY
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
self.assertFalse(err)
# copy a MET to a HIS
err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
self.assertFalse(err)
# copy a GLY to a MET with adding CB
err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
self.assertFalse(err)
residues = new_hdl.residues
self.assertEqual(len(residues), 8)
# MET to MET
self.assertTrue(residues[0].FindAtom("CB").IsValid())
#GLY to GLY
self.assertFalse(residues[1].FindAtom("CB").IsValid())
#now we copy a GLY to a GLY
self.assertFalse(residues[2].FindAtom("CB").IsValid())
#now we copy a HIS to a HIS
self.assertTrue(residues[3].FindAtom("CB").IsValid())
#now we copy a GLY to a HIS without adding CB
self.assertFalse(residues[4].FindAtom("CB").IsValid())
#now we copy a MET to a GLY
self.assertFalse(residues[5].FindAtom("CB").IsValid())
# copy a MET to a HIS
self.assertTrue(residues[6].FindAtom("CB").IsValid())
# copy a GLY to a MET with adding CB
self.assertTrue(residues[7].FindAtom("CB").IsValid())
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound library available. Ignoring test_nonstandard.py tests.')
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